--
Hello Elmer,
Unfortunately the annotation we have for the cow genome is somewhat limited, which constrains your options if you're set on comparing data from corresponding tables between the cow and human genomes. Your only option may be to use the tRNA and rRNA data from the rmsk table as described in the link you provided. Whether this is appropriate for your research is a question that goes beyond the scope of this mailing list - it will depend on the specific question you're trying to ask and how the datasets were originally constructed.
Using RepeatMasker data may well be enough for your initial rough comparison. Following the instructions in the link you provided generates about 2000 tRNA records from the human rmsk table. This is rather larger than the ~600 in the predicted tRNAs track, but at least appears to cover all but 34 of the predicted items. For more information about RepeatMasker data you can consult their website at www.repeatmasker.org.
As an alternative for tRNA data, you can run the same prediction software on the cow genome that we used to generate the human tRNAs track. More information about that track and its creation is available on the track description page here: http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=tRNAs. A similar project involving other organisms is described in this paper:
Goodenbour JM, Pan T. Diversity of tRNA genes in eukaryotes. Nucleic Acids Res. 2006;34(21):6137-46. PMID: 17088292; PMC: PMC1693877.
http://nar.oxfordjournals.org/content/34/21/6137
Chromosome M annotation is similarly limited, particularly for the cow genome. You may be able to obtain some results by taking the the Gencode chromosome M annotation from the human genome and searching for those sequences in cow with an alignment tool like BLAT (http://genome.ucsc.edu/cgi-bin/hgBlat). BLAT has difficulty aligning repetitive sequences like rRNAs and tRNAs, but should have less trouble finding matches for mitochondrial sequences.
I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
--
Jonathan Casper
UCSC Genome Bioinformatics Group
--
1. Select “Mammal”, “Cow”, “Oct 2011 (Baylor Btau_4.6.1/bosTau7)”
2. Group: Genes and Gene Prediction Tracks
3. Track: RefSeq Genes
4. Table: Cow ESTs (All ESTs)
5. Output format: GTF – gene transfer format
6. Filename: bosTau7_GenesNGenePredictions_RefSeq_CowESTs.gtf
7. Click "region"
8. Select mitochondria with: ‘chrM’ in the ‘position’ field and click 'lookup'.
9. Click ‘get output’ on that page
Hello Elmer,
That is certainly a legal thing to do from the perspective of the Table Browser. Whether examining ESTs is appropriate for your research is a question that really only you can answer. The steps you describe will give you a list of all ESTs from the all_est table that appear in chromosome M of the cow genome. You can also access this table from the track group "mRNA and EST Tracks", track "Cow ESTs", table "all_est". In that same group of tracks we have a related "spliced ESTs" track that may be useful to you - it contains only those ESTs that show evidence of at least one canonical intron. More information about that track is available here: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=bosTau7&g=intronEst.
You may also be interested in the answers to these mailing list questions: https://groups.google.com/a/soe.ucsc.edu/d/topic/genome/zR-BFms-lEk/discussion,https://groups.google.com/a/soe.ucsc.edu/d/topic/genome/-JMFaCvkUBM/discussion.
I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
--
Jonathan Casper
UCSC Genome Bioinformatics Group
--